Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Daniel J Butler; Christopher Mozsary; Cem Meydan; David C Danko; Jonathan Foox; Joel Rosiene; Alon Shaiber; Ebrahim Afshinnekoo; Matthew MacKay; Fritz J Sedlazeck; Nikolay A Ivanov; Maria A Sierra; Diana Pohle; Michael Zeitz; Vijendra Ramlall; Undina Gisladottir; Craig D Westover; Krista Ryon; Benjamin Young; Chandrima Bhattacharya; Phyllis Ruggiero; Bradley W Langhorst; Nathan A Tanner; Justyn Gawrys; Dmitry Meleshko; Dong Xu; Jenny Xiang; Angelika Iftner; Daniela Bezdan; John Sipley; Lin Cong; Arryn Craney; Priya Velu; Ari Melnick; Iman A Hajirasouliha; Thomas Iftner; Mirella Salvatore; Massimo Loda; Lars F Westblade; Shawn Levy; Melissa Cushing; Nicholas P Tatonetti; Marcin Imielinski; Hanna Rennert; Christopher Mason

Fragment assembly was also performed using IRMA (Sehpard et al., 2016) . The Wuhan-Hu-1 genome (Genbank accession MN908047.3) was used as a reference with the poly-A tail trimmed to reduce the likelihood of false low-complexity matching. An HMM model of this reference sequence was created using the native modelfromalign script. IRMA was run with the COV module with the following parameters adjusted from the default: minimum read length = 25bp; minimum read pattern count = 5; minimum read count = 2; minimum count for alternative finished assembly = 20. Consensus assemblies were aligned to the Wuhan-Hu-1 reference using MAFFT (Katoh and Standley, 2013) with default settings, and sequence identity and coverage metrics were calculated using Mview (Brown et al., 1998) . Phylogenetic trees were created using nextstrain's augur as described above, and visualized using the ggtree package in R (Yu, 2020) .